The subject of the study is environmental and economic systems. The authors specified the concept of environmental and economic systems as the natural environment under the influence of human economic and social activities, including mutual influence, as well as the consequences resulting from it. The authors set a goal to develop a methodology for the study of environmental and economic systems that would adequately assess their current state and forecast changes. The approach to the study of such systems consists in the staged application of cluster analysis and data mining classification methods (random forest and support vectors method) and followed assessment of the quality of the model and choosing the best method. In presented research, the analytical procedures are automated in the R-Studio package. The analysis of the same indicators by two different methods confirmed the direct relationship between the costs and investments in environmental protection and the results of environmental protection: with the growth of investments in environmental protection, indicators of recycled water use, discharge of polluted wastewater, air emissions of pollutants were reduced.